The key genetic regulator, promoter, usually determines the ultimate fate of gene transcription. The structure of eukaryotic promoter is modular comprising a distal upstream activating sequence (UAS) and a proximal core promoter containing TATA element. Both distal and proximal regions are embedded with a number of cis elements which acts as the binding sites of different transcription factors and transcription binding proteins (TBPs) while RNA polymerase binds to the proximity of TATA box. The combinatorial/spatial interactions between cis and trans factor along with the cross talk between the proximal and distal part of promoter usually determines the functional characteristics of the promoter and regulate the gene transcription (Goodrich and Tjian, 2010; Lee and Young, 2000). Based upon these factors, redesigning of promoter structure by genetic manipulations could be possible to develop a better promoter with altered cis-profiles/cis-arrangements. Such ‘tailor-promoter’ usually holds better promise for developing plant of interest in comparison to the native promoter. Exchanging/swapping/shuffling the proximal and distal domains among different native (plant/animal) promoter sequences, one can develop unique recombinant promoter-module that manifest functional properties combining the features of both donating and receiving promoters (Venter and Botha, 2010; Bhullar et al., 2003; Venter, 2007). Several engineered/modified promoters were developed in recent past (Comai et al., 1990, Ni et al., 1995; Lee et al., 2007; Rushton et al., 2002; Venter, 2007). The present inventors have developed several useful plant promoters using both full-length transcript (Flt-) and sub-genomic transcript (Sgt-) promoters from different members of pararetrovirus (Kumar et al., 2011; Ranjan et al., 2012; Patro et al., 2012, Kumar et al., 2012). Unfortunately, the availability of such engineered promoters is not sufficient to meet their current demand in plant molecular biology and there is a constant shortage of such promoter in plant molecular biology.
Again, in eukaryotes a single gene requires a promoter for its expression. Therefore, during gene stacking or gene pyramiding, one needs to use multiple numbers of heterologous promoters for expression multiple numbers of genes. There is possibility of promoter sequence homology based genetic rearrangement/recombination in case of repeated use of same promoter for expressing multiple number of gene in plant cell. In such cases, use of different heterologous promoters could be advantageous over multiple use of same promoter as it was documented that homologous sequences, more than 90 bp between two promoters often lead to gene silencing in transgenic plants (Flavell, 1994).